Adaptation to diverse nitrogen-limited environments by deletion or extrachromosomal element formation of the GAP1 locus
Adaptation to diverse nitrogen-limited environments by deletion or extrachromosomal element formation of the GAP1 locus
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DOI：
10.1073/pnas.1014023107
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发表时间：
2010-10-26
影响因子：
11.1
通讯作者：
Regenberg, Birgitte
中科院分区：
文献类型：
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作者：
Gresham, David;Usaite, Renata;Regenberg, Birgitte
为了研究在特定环境中的适应性进化，我们用酿酒酵母(酵母)在氮限制的恒化器培养中进行了进化实验。我们使用DNA微阵列来识别与适应相关的拷贝数变异，并观察到Gap1基因座频繁的扩增和缺失。GAP1编码一般的氨基酸渗透酶，该酶负责跨质膜运输氨基酸。我们鉴定了一种自繁殖的染色体外环状DNA分子，它是由Gap1侧翼的长末端重复序列(Ltrs)之间的染色体内重组产生的。染色体外DNA环(Gap1(环))包含Gap1、复制起点ARS1116和来自两个侧翼LTRs之间重组的单个杂交LTR。Gap1(环)的形成与染色体Gap1(Gap1 Delta)的缺失和在Gap1染色体上产生单个杂交LTR有关。GAP1环是在L谷氨酰胺限制的化学恒化器中长期培养后选择的，其方式类似于在人类癌症中双分钟出现的癌基因的选择。只携带Gap1 Delta等位基因的克隆在不同的非氨基酸氮限制下进行选择，包括铵、尿素和尿囊素限制。先前的研究表明，串联重复序列之间的染色体内重组的速度是由插入序列的转录刺激的。在氮限制的恒化器中，Gap1的高水平表达表明，在氮限制条件下，GAP1循环和Gap1 Delta的产生频率可能会增加。我们认为，这种基因组结构有助于酿酒酵母种群在环境氮素水平和来源的变化下的进化。
To study adaptive evolution in defined environments, we performed evolution experiments with Saccharomyces cerevisiae (yeast) in nitrogen-limited chemostat cultures. We used DNA microarrays to identify copy-number variation associated with adaptation and observed frequent amplifications and deletions at the GAP1 locus. GAP1 encodes the general amino acid permease, which transports amino acids across the plasma membrane. We identified a self-propagating extrachromosomal circular DNA molecule that results from intrachromosomal recombination between long terminal repeats (LTRs) flanking GAP1. Extrachromosomal DNA circles (GAP1(circle)) contain GAP1, the replication origin ARS1116, and a single hybrid LTR derived from recombination between the two flanking LTRs. Formation of the GAP1(circle) is associated with deletion of chromosomal GAP1 (gap1 Delta) and production of a single hybrid LTR at the GAP1 chromosomal locus. The GAP1circle is selected following prolonged culturing in L-glutamine-limited chemostats in a manner analogous to the selection of oncogenes present on double minutes in human cancers. Clones carrying only the gap1 Delta allele were selected under various non-amino acid nitrogen limitations including ammonium, urea, and allantoin limitation. Previous studies have shown that the rate of intrachromosomal recombination between tandem repeats is stimulated by transcription of the intervening sequence. The high level of GAP1 expression in nitrogen-limited chemostats suggests that the frequency of GAP1circle and gap1 Delta generation may be increased under nitrogen-limiting conditions. We propose that this genomic architecture facilitates evolvability of S. cerevisiae populations exposed to variation in levels and sources of environmental nitrogen.